Where to find expected copy number for a gene

Question

[LayneSadler]

Is there a reference database where I can find the expected copy number of a given gene in the human germline genome?

It is my understanding that most human genes have 1 copy on each chromosome. However, there are genes that are commonly deleted or duplicated.

In other organisms I know elephants have many copies of TP53.

Answer 1

[GenoMax]

Based on the current gene annotation found in https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.annotation.gtf.gz one can count the gene name entries that are labeled "protein_coding" using a small script

$ more gene.sh
#!/bin/bash
awk '$3 == "gene" && $0 ~ /gene_type "protein_coding"/ {
    match($0, /gene_name "([^"]+)"/, arr)
    print arr[1]
}' "$1" | sort | uniq -c | sort -nr

If you run the script using the file above, you can count gene entries (Note: these are protein coding genes).

./gene.sh gencode.v48.annotation.gtf > human_genes

There are only a few two copy genes (where are rest appear to be single copy).

      2 ZBED1
      2 WASH6P
      2 VAMP7
      2 SLC25A6
      2 SHOX
      2 PPP2R3B
      2 POLR2J3
      2 PLCXD1
      2 PINX1
      2 PDE8B
      2 PDE4C
      2 P2RY8
      2 MATR3
      2 KYAT1
      2 IL9R
      2 IL3RA
      2 HERC3
      2 GTPBP6
      2 FAM174C
      2 DUSP13B
      2 DHRSX
      2 CSF2RA
      2 CRLF2
      2 CD99
      2 C4orf36
      2 ASMTL
      2 ASMT
      2 AKAP17A